Differential Gene Expression Analysis

The R package Deseq2 (Version: 1.38.3) (23) was used to determine differential gene expression. We used variance stabilizing transformations for raw data transformation, transformed the data on the log₂ scale, and normalized it to library size. We used the Anan empirical Bayes shrinkage methods to detect and correct for dispersion and calculate log₂[fold change] for the genes. Differentially expressed genes were defined as having a |log₂[fold change]| of greater than 1. The p values were corrected for multiple testing using the Benjamini-Hochberg procedure. A false discovery rate (FDR) of less than 0.05 was considered significant.